Three-dimensional arrangement of chromatin in the nucleus of eukaryotic cells is important in the regulation of gene expression. However, so far the methods that can address this arrangement of chromatin in the nucleus have been inefficient. Current methods are limited to assaying two select loci or loci that interact with one particular locus at a time, while being able to determine the spatial organization of all loci at the same time is highly demanded.
Since the 1980s fluorescence microscopy and related techniques have been used to study the overalls of nuclear architecture (Science 1998 Apr. 24; 280(5363):547-53). However, these techniques suffer from low resolution and low throughput. In 2002, Dekker and colleagues introduced the so-called 3C (Chromosome Conformation Capture) technology that allows for quantitative and higher resolution characterization of the spatial arrangement of loci relative to each other in a chromatin context (Science 2002; 295(5558):1306-11). This technique has been used to investigate the functional relevance of the spatial arrangement of loci relative to each other in many instances (e.g., Spilianakis C G et al. Nature 2005; 435(7042):637-45). Since 3C suffers low throughput (only two loci can be analyzed at a time), variations of this technology have been developed to improve efficiency. These variations are often referred to as 4C or 5C (Dostie J et al. Genome Res. 2006; 16(10):1299-309; Simonis M et al. Nat Genet. 2006; 38(11):1348-54; and Zhao Z et al. Nat Genet. 2006; 38(11):1341-7). All the mentioned techniques, in spite of improved throughput, are unable to solve the entire spatial arrangement of the chromatin in nucleus and therefore have to focus on capturing interaction partners of a limited number of loci.